diff --git a/debug_pvc.nf b/debug_pvc.nf new file mode 100644 index 0000000..979a751 --- /dev/null +++ b/debug_pvc.nf @@ -0,0 +1,45 @@ +#!/usr/bin/env nextflow +nextflow.enable.dsl=2 + +params.outdir = '/omic/eureka/digital-patients' + +process DEBUG_PVC { + container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest' + + script: + """ + echo "=== PVC mount check ===" + echo "Current dir: \$(pwd)" + echo "" + echo "=== /omic/eureka contents ===" + ls -la /omic/eureka/ 2>&1 | head -20 + echo "" + echo "=== /omic/eureka/digital-patients/ ===" + ls -la /omic/eureka/digital-patients/ 2>&1 | head -30 + echo "" + echo "=== /omic/eureka/digital-patients/imputed/ ===" + ls -la /omic/eureka/digital-patients/imputed/ 2>&1 | head -20 + echo "" + echo "=== /omic/eureka/digital-patients/healthy/ ===" + ls -la /omic/eureka/digital-patients/healthy/ 2>&1 | head -20 + echo "" + echo "=== /omic/eureka/digital-patients/supporting-data/ ===" + ls -laR /omic/eureka/digital-patients/supporting-data/ 2>&1 | head -30 + echo "" + echo "=== Check for assembled files ===" + ls -lh /omic/eureka/digital-patients/imputed/F5_SCHIZO* 2>&1 + ls -lh /omic/eureka/digital-patients/healthy/gnomad* 2>&1 + ls -lh /omic/eureka/digital-patients/supporting-data/genome/hg38* 2>&1 + echo "" + echo "=== Small files check ===" + ls -lh /omic/eureka/digital-patients/MANE* 2>&1 + ls -lh /omic/eureka/digital-patients/regulon* 2>&1 + ls -lh /omic/eureka/digital-patients/LM22* 2>&1 + ls -lh /omic/eureka/digital-patients/ukbb* 2>&1 + echo "=== DEBUG COMPLETE ===" + """ +} + +workflow { + DEBUG_PVC() +}